An InDel-based linkage map of hot pepper (Capsicum annuum).
An InDel-based linkage map of hot pepper (Capsicum annuum).
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基于 InDel 的辣椒 (Capsicum annuum) 连锁图谱
DOI：
10.1007/s11032-015-0219-3
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Hu K
中科院分区：
文献类型：
--
作者：
Li W;Cheng J;Wu Z;Qin C;Tan S;Tang X;Cui J;Zhang L;Hu K
最近，两个独立的辣椒基因组被公布，开启了辣椒分子遗传学研究的新纪元。然而，辣椒分子标记技术仍主要集中在来自公共数据库或基因组文库的简单重复序列上。单核苷酸多态性、结构变异和插入/缺失多态性（InDels）等第三代标记系统的开发和应用尚处于起步阶段。本研究利用辣椒自交系BA 3（C. annuum）和B702（C. annuum）。通过将重测序读数与Zunla-1参考基因组比对，分别鉴定了BA 3和B702的总共154，519和149，755个InDel（1-5 bp）位点。然后，预测了BA 3和B702之间不同的14，498个InDel位点（仅4和5 bp）。最后，在一组随机的1，000个引物对中，验证了251个InDel标记，并使用来自种内杂交BA 3 × B702的F2群体将其绘制到连锁图谱上。第一张InDel图谱由12个连锁群组成，遗传距离为1178.01cM，标记间平均距离为5.01cM。与Zunla-1参考物理图谱相比，在所有12条染色体上观察到高度一致性，该图谱覆盖的骨架锚定总长度和物理距离分别为299.66和2，558.68 Mb，分别占Zunla-1参考基因组（3.35 Gb）的8.95%和76.38%。此外，来自当前基因组组装的假染色体（P0）的37个支架（总长度为36.21 Mb）通过40个InDel标记被新分配到相应的染色体。因此，该图谱提供了良好的基因组覆盖率，将有助于辣椒的基础和应用研究。
Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker system such as single nucleotide polymorphisms, structure variations as well as insertion/deletion polymorphisms (InDels) is still in its infancy. In the present study, we developed InDel markers for pepper genetic mapping with the convenience of two whole-genome re-sequenced inbred lines BA3 (C. annuum) and B702 (C. annuum). A total of 154,519 and 149,755 InDel (1–5 bp) sites were identified for BA3 and B702, respectively, by the alignment of re-sequencing reads to Zunla-1 reference genome. Then, 14,498 InDel sites (only 4 and 5 bp) that are different between BA3 and B702 were predicted. Finally, within a random set of 1,000 primer pairs, 251 InDel markers were validated and mapped onto a linkage map using F2population derived from the intraspecific cross BA3 × B702. The first InDel-based map, named as BB-InDel map, consisted of 12 linkage groups, covered a genetic distance of 1,178.01 cM and the average distance between bin markers was 5.01 cM. Compared to the Zunla-1 reference physical map, high consistency was observed on all 12 chromosomes, and the total length of scaffold anchored and physical distance covered by this map was 299.66 and 2,558.68 Mb, respectively, which accounted for 8.95 and 76.38 % of the Zunla-1 reference genome (3.35 Gb), respectively. Furthermore, 37 scaffolds (total length of 36.21 Mb) from the pseudo-chromosome (P0) of the current genome assembly were newly assigned to the corresponding chromosomes by 40 InDel markers. Thus, this map provided good genome coverage and would be useful for basic and applied research in pepper.
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影响因子：
1.9
作者：
Huang, SW;Zhang, BX;Guo, JZ
通讯作者：
Guo, JZ
影响因子：
1.9
作者：
LANTERI, S;PICKERSGILL, B
通讯作者：
PICKERSGILL, B
影响因子：
2.4
作者：
Mimura Y;Inoue T;Minamiyama Y;Kubo N
通讯作者：
Kubo N
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影响因子：
3.7
作者：
Liu, Ping;Cai, Xing-Xing;Lu, Bao-Rong
通讯作者：
Lu, Bao-Rong
影响因子：
2.8
作者：
Lu, Fu-Hao;Cho, Myeong-Cheoul;Park, Yong-Jin
通讯作者：
Park, Yong-Jin